Development and assessment of simple PCR markers for SNP genotyping in barley.

Simple molecular marker assays underpin routine plant breeding and research activities in many laboratories worldwide. With the rapid growth of single nucleotide polymorphism (SNP) resources for many important crop plants, the availability of routine, low-tech marker assays for genotyping SNPs is of increased importance. In this study, we demonstrate that temperature-switch PCR (TSP) supports the rapid development of robust, allele-specific PCR markers for codominant SNP genotyping on agarose gel. A total of 87 TSP markers for assessing gene diversity in barley were developed and used to investigate the efficacy for marker development, assay reliably and genotyping accuracy. The TSP markers described provide good coverage of the barley genome, are simple to use, easy to interpret and score, and are amenable to assay automation. They provide a resource of informative SNP markers for assessing genetic relationships among individuals, populations and gene pools of cultivated barley (Hordeum vulgare L.) and its wild relative H. spontaneum K. Koch. TSP markers provide opportunities to use available SNP resources for marker-assisted breeding and plant genetic research, and to generate information that can be integrated with SNP data from different sources and studies. TSP markers are expected to provide similar advantages for any animal or plant species.

Definition of polymorphisms in the gene encoding the interleukin-12 receptor B1 subunit: testing linkage disequilibrium with Type I diabetes susceptibility.

The cytokine interleukin (IL)-12 is bound by a heterodimeric receptor and mediates a range of immunological activities, in particular, favouring the development of uncommitted T cells to the Th1 phenotype. Genes encoding elements of the IL-12 pathway are therefore good candidates for mediating susceptibility or resistance to a range of immune disorders, including Type I diabetes. We made a systematic search for variants in the human gene encoding the low-affinity IL-12 receptor, IL12RB1. Four single-nucleotide polymorphisms and two microsatellite polymorphisms were defined. We also tested these IL12RB1 alleles for involvement in Type I diabetes susceptibility, testing 131 families. Although suggestive evidence for linkage to a susceptibility gene was found, none of the IL12RB1 variants we defined demonstrated preferential transmission in these families.

The relationship between antibiotic residue violations and somatic cell counts in Wisconsin dairy herds.

The objective of this retrospective observational study was to characterize somatic cell counts (SCC) on Wisconsin dairy farms and to determine the relationship between SCC and the risk of antibiotic residue violation. Monthly official state regulatory data were used when both the bulk tank SCC value and antibiotic test results were available for the same date. Data were collected from Wisconsin dairy farms from January 1995 through November 1998 and consisted of results of tests performed on 805,772 grade A and 176,763 grade B milk samples. Herd-year SCC averages were used to classify herds (< or =250,000; 251,000 to 400,000, 401,000 to 550,000, 551,000 to 700,000, >700,000), and the relative risk of antibiotic residue by SCC class was determined. Arithmetic mean SCC values were 334,634 and 480,029 for grade A and grade B milk, respectively. SCC values were significantly higher for samples with positive antibiotic residue tests for grade A milk during all 4 yr tested. The SCC values were significantly higher for samples with positive antibiotic residue tests for grade B milk for 3 of 4 yr. The rate of antibiotic residue violation per 1000 herd-years increased with SCC class for both grade A and grade B milk. The relative risks of antibiotic residue violation by SCC class were 1.0, 1.43, 2.38, 2.78, and 7.10 for grade A milk and 1.0, 1.11, 2.67, 4.33, and 5.43 for grade B milk. Programs to reduce the level of subclinical mastitis on dairy farms may have an additional benefit of reducing the risk of antibiotic residue violations.

Response of Ulmus americana seedlings to varying nitrogen and water status. 2 Water and nitrogen use efficiency in photosynthesis.

Photosynthetic utilization of water and nitrogen in Ulmus americana L. seedlings was tightly linked with the relative availability of each resource. During periodic drying cycles, water use efficiency increased as predawn water potential fell from -0.5 to -2.0 MPa. During the later stages of such drying cycles, the relative contribution of stomatal limitations to the total net photosynthetic limitation appeared to be at its greatest, whereas biochemical limitations were predominant in well-watered plants grown under low nitrogen (N) availability. For any level of leaf water status, water use efficiency of photosynthesis (WUE) was always greater in plants with high leaf N content than in plants with low leaf N content. Photosynthetic nitrogen use efficiency (PNUE) was always greater in plants with low leaf N content than in plants with high leaf N content, for any level of water status. In combined N treatments and predawn water status classes, there was a significant inverse relationship between PNUE and WUE.